From an IGN interview with Joe Rhode:
Asked whether other characters were considered for the ride before the Guardians, Rohde replied, “Very early in any conceptual exploration, you float these ideas. There’s a lot of Marvel characters you can imagine. You’re like, ‘Oh, Spider-Man!’ But there’s a super compressed little space. And you’re like, ‘What is he doing in this tiny little space?!’ Usually what happens is you hit on something and a bunch of little dominoes go clack, clack, clack and then, ‘That’s going to work!
It sounds like the ride was assigned to imagineers well before a new theme was settled upon. I don't have a hard time believing that the powers that be felt Tower was an easy choice to change out. Consider from their view: the nature of the ride system would narrow the possibilities for alteration(read: reasonable budget), the perceived draw of the ride was the thrill so the theme could be fluid, and it was close to potential expansion space for future marvel attractions. I'm more inclined to think the ride is popular, but that made it all the more attractive as a candidate for change. It's a low risk proposition.
(By the way, being new to these parts I'm not totally sure that I did right quoting another site like that. If it's uncouth let me know)